Contacts of the helix formed by residues 85 - 96 (chain B) in PDB entry 5AM8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.3 13.5 + - - +
18B GLN* 2.9 25.7 + - - +
83B PHE* 3.3 1.1 - - - +
84B THR* 1.3 79.1 + - - +
86B PRO* 1.4 64.7 - - - +
87B GLN* 3.0 24.2 + - - +
88B LEU* 3.2 18.7 + - + +
89B ARG* 3.1 29.1 + - - +
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR 3.5 9.2 - - - +
85B ASP* 1.4 86.8 - - - +
87B GLN* 1.3 64.2 + - + +
89B ARG* 3.3 35.2 + - - +
90B ARG* 3.3 32.2 + - - +
549B SER 5.0 8.5 - - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 3.0 11.7 + - - +
86B PRO* 1.3 76.1 - - + +
88B LEU* 1.3 61.9 + - - +
90B ARG* 3.2 6.0 + - - +
91B ILE* 2.9 38.3 + - + +
375B LEU* 4.0 18.6 - - - +
376B PRO* 3.7 16.5 - - - +
379B LEU* 3.6 24.8 - - + +
549B SER* 3.9 24.8 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 4.0 17.5 - - + +
17B ALA* 3.6 30.3 - - + +
18B GLN* 3.7 33.0 - - + +
21B ALA* 3.9 16.8 - - + -
83B PHE* 3.9 19.5 - - + -
85B ASP* 3.2 22.3 + - + +
87B GLN* 1.3 80.2 - - - +
89B ARG* 1.3 61.4 + - - +
91B ILE* 3.3 8.3 + - + +
92B ILE* 3.1 40.8 + - + +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 3.2 39.0 - - + +
81B GLN* 3.4 24.8 + - - +
83B PHE* 3.0 27.3 + - + +
84B THR 4.9 2.2 + - - -
85B ASP 3.1 10.6 + - - +
86B PRO* 3.3 45.4 + - - +
87B GLN 3.2 0.4 - - - -
88B LEU* 1.3 76.2 - - - +
90B ARG* 1.3 63.9 + - + +
92B ILE* 3.4 2.1 + - - -
93B GLY 3.0 24.6 + - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 5.3 1.1 - - - -
86B PRO* 3.3 20.2 + - - +
87B GLN* 3.2 5.3 + - - +
89B ARG* 1.3 83.4 - - + +
91B ILE* 1.3 64.3 + - - +
93B GLY* 3.9 1.7 - - - +
94B ALA* 3.1 24.4 + - - +
203B ASN* 6.1 1.4 - - - +
379B LEU* 4.0 15.9 - - + +
383B ALA 5.2 3.8 + - - -
548B SER* 2.8 35.3 + - - +
549B SER* 3.4 16.1 + - - +
550B ARG 3.5 18.4 + - - -
551B PRO* 3.8 26.9 - - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 6.1 1.3 - - + -
21B ALA* 4.0 33.4 - - + +
24B TYR* 5.0 5.2 - - + -
87B GLN* 2.9 28.2 + - + +
88B LEU* 3.3 11.4 + - + +
90B ARG* 1.3 76.6 - - - +
92B ILE* 1.3 66.0 + - + +
94B ALA* 3.4 1.9 + - - +
95B VAL* 3.1 36.0 + - + +
376B PRO* 3.5 38.1 - - + -
378B SER* 4.0 24.2 + - - +
379B LEU* 4.3 5.4 - - + -
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA* 3.8 9.0 - - + +
20B PHE* 4.8 13.9 - - + -
72B ALA* 4.6 13.5 - - + +
76B TYR* 4.3 20.6 - - + -
80B TRP* 3.6 28.9 - - + -
83B PHE* 3.7 28.3 - - + -
88B LEU* 3.1 42.7 + - + +
89B ARG 4.0 2.7 - - - +
91B ILE* 1.3 75.8 - - + +
93B GLY* 1.3 66.0 + - - +
95B VAL* 3.2 5.9 + - - +
96B ARG* 2.9 26.7 + - - +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 3.4 31.0 - - - -
89B ARG 3.0 11.6 + - - -
90B ARG* 3.5 2.7 + - - -
92B ILE* 1.3 76.9 - - - +
94B ALA* 1.3 59.8 + - - +
96B ARG* 3.2 14.7 + - - +
97B THR* 3.1 17.2 + - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ARG 3.1 19.0 + - - +
91B ILE 3.7 4.0 - - - +
93B GLY* 1.3 73.4 - - - +
95B VAL* 1.3 66.4 + - + +
97B THR* 3.1 25.3 + - - +
378B SER* 4.2 20.4 - - - +
381B ARG* 4.4 15.9 - - - +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.3 7.9 - - + -
24B TYR* 3.6 50.7 - - + +
65B ALA 4.6 2.1 - - - +
68B TRP* 3.6 29.4 - - + +
69B GLY* 3.4 13.2 + - - +
72B ALA* 3.9 9.9 - - + -
91B ILE* 3.1 24.6 + - + +
92B ILE* 3.2 6.9 + - - +
94B ALA* 1.3 75.9 - - - +
96B ARG* 1.3 60.8 + - - +
97B THR 3.2 6.5 + - - +
98B LEU* 4.3 0.5 - - - +
378B SER* 4.2 4.5 - - - +
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY 4.4 10.1 - - - +
72B ALA* 4.8 6.3 - - + +
73B LYS* 3.2 48.0 + - + +
77B GLU* 2.8 40.6 + - - +
80B TRP* 3.7 37.9 - - - +
92B ILE* 2.9 17.9 + - + +
93B GLY* 3.2 15.7 + - - +
95B VAL* 1.3 75.8 - - - +
97B THR* 1.3 62.5 + - - +
98B LEU* 3.5 6.8 + - - +
189B ASP* 4.2 8.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il